Antisense polynucleotides are useful for specifically inhibiting unwanted gene expression in mammalian cells. They can be used to hybridize to and inhibit the function of an RNA, typically a messenger RNA, by activating RNAse H.
The use of antisense oligonucleotides has emerged as a powerful new approach for the treatment of certain diseases. The preponderance of the work to date has focused on the use of antisense oligonucleotides as antiviral agents or as anticancer agents (Wickstrom, E., Ed., Prospects for Antisense Nucleic Acid Therapy of Cancer and AIDS, New York: Wiley-Liss, 1991; Crooke, S. T. and Lebleu, B., Eds., Antisense Research and Applications, Boca Raton: CRC Press, 1993, pp. 154-182; Baserga, R. and Denhardt, D. T., 1992, Antisense Strategies, New York:. The New York Academy of Sciences, Vol. 660; Murray, J. A. H., Ed., Antisense RNA and DNA, New York: Wiley-Liss, 1993).
There have been numerous disclosures of the use of antisense oligonucleotides as antiviral agents. For example, Agrawal et al. report phosphoramidate and phosphorothioate oligonucleotides as antisense inhibitors of HIV. Agrawal et al., Proc. Natl. Acad. Sci. USA 85, 7079-7083 (1988). Zamecnik et al. disclose antisense oligonucleotides as inhibitors of Rous sarcoma virus replication in chicken fibroblasts. Zamecnik et al., Proc. Natl. Acad. Sci. USA 83, 4143-4146 (1986).
The principal mechanism by which antisense oligonucleotides affect the level of the target RNA is by activation of RNAse H, which cleaves the RNA strand of DNA/RNA hybrids. Both phosphodiester and phosphorothioate-linked DNA activates endogenous RNAse H, thereby cleaving the targeted RNA (Agrawal, S., et al., Proc. Natl. Acad. Sci. USA 87, 1101-5 (1990); Woolf, T. M., et al., Nucleic Acids Res. 18, 1763-9 (1990)). However, phosphodiester-linked DNA is rapidly degraded by cellular nucleases and, with the exception of the phosphorothioate-linked DNA, nuclease resistant, non-naturally occurring DNA derivatives do not activate RNAse H when hybridized to RNA. While phosphorothioate DNA has the advantage of activating RNAse H, phosphorothioate-linked DNA has non-specific cytotoxic effects and also has reduced affinity for RNA (Stein, C. A., et al., Aids Res Hum Retroviruses 5, 639-46 (1989); Woolf, T. M., et al., Nucleic Acids Res. 18, 1763-9 (1990); Kawasaki, A. M., et al., J. Med. Chem. 36, 831-41 (1993)).
Chimeric antisense oligos that have a short stretch of phosphorothioate DNA (3-9 bases) have been used to obtain RNAse H-mediated cleavage of the target RNA (Dagle, J. M., et al., Nucleic Acids Res. 18, 4751-7 (1990); Agrawal, S., et al., Proc. Natl. Acad. Sci. USA 87, 1401-5 (1990); Monia, B. P. et al., 1993, J. Biol. Chem. 268, 14514) A minimum of 3 DNA bases is required for activation of bacterial RNAse H (Futdon, P. J., et al., Nucleic Acids Res. 17, 9193-9204; Quartin, R. S., et al., Nucleic Acids Res. 17, 7235-7262) and a minimum of 5 bases is required for mammalian bacterial RNAse H activation (Monia, B. P., et al., J. Biol. Chem. 268, 14514-14522 (1993)). In these chimeric oligonucleotides there is a central region that forms a substrate for RNAse H that is flanked by hybridizing “arms,” comprised of modified nucleotides that do not form substrates for RNAse H. Alternatively, extracellular tests using a RNAse H-containing HeLa cell extract have been reported wherein the RNAse H activating region was placed on the 5′ or 3′ side of the oligomer. Specifically these tests reported that a 5′ or 3′ terminal RNAse H activating region composed of phosphodiester 2′-deoxynucleotides joined to a methylphosphonate-linked complementarity region was fully active, but that a 5′ terminal RNAse H-activating region composed of phosphorothioate 2′-deoxynucleotides joined to a methylphosphonate-linked complementarity region was only partially active. See Col 10, U.S. Pat. No. 5,220,007 to T. Pederson et al.
2′-O-Methyl or 2′-fluoro modified nucleotides have been used for the hybridizing arms of chimeric oligos. Inoue, H., et al., 1987, Nucleic Acids Res. 15, 6131-48. The 2′-O-Methyl group increases the affinity of the oligomer for the targeted RNA and increases the activity of the oligomer in cell culture. However, 2′-O-Methyl bases with phosphodiester linkages are degraded by exonucleases and so are not suitable for use in cell or therapeutic applications of antisense. Shibahara, S., et al., 1989, Nucleic Acids Res. 17, 239-52. Phosphorothioate 2′-O-Methyl nucleotides are resistant to nucleases as shown in the uniformly phosphorothioate modified oligos described by Monia B. P., et al., 1993, J. Biol. Chem. 268, 14514-14522 and terminal phosphorothioate substituted, 2′-O-Methylribo-oligonucleotides, Shibahara, S., et al., 1989, Nucleic Acid Res. 17, 239-252. However, fully phosphorothioate substituted oligomers may cause non-specific effects including cell toxicity. Stein, C. A., et al., 1989, Aids Res. Hum. Retrov. 5, 639-646; Woolf, T. M., et al., 1990, Nucleic Acids Res. 18,1763-69; Wagner, R. W., 1995, Antisense Res. Dev. 5, 113-115; Krieg, A. M., & Stein, C. A., 1995, Antisense Res. Dev. 5, 241. The effects of 2′-Fluoro-oligonucleotides on bacterial RNase H are discussed in Crooke, S. T. et al., 1995, Bioch. J. 312, 599-608 and Iwai, S. et al., 1995, FEBS Lett. (Neth.) 368, 315-20.
Several other chemistries have been used to make the “arms” or regions of a chimeric oligomer that are not substrates for RNAse H. The first chimeric oligomers used methylphosphonate or phosphoramidate linkages in the arms (Dagle, J. M., Walder, J. A. & Weeks, K. L., Nucleic Acids Res. 18, 1751-7 (1990); Agrawal, S., et al., Proc. Natl. Acad. Sci. USA 87, 1401-5 (1990). While these compounds functioned well in buffer systems and Xenopus oocytes, the arms decreased the hybrid affinity. This decrease in affinity dramatically reduces the activity of oligomers in mammalian cell culture.
A number of studies have been reported for the synthesis of ethylated and methylated phosphotriester oligonucleotides and their physico-chemical and biochemical evaluation. Dinucleotides with methyl and ethyl triesters were shown to possess greater affinity towards polynucleotides possessing complementary sequences (Miller, P. S., et al., J. Am. Chem. Soc. 93, 6657, (1971)). However, a few years ago, another group reported lack of, or poor binding affinity of heptethyl ester of oligothymidine with complementary polynucleotides (Pless, R. C., and Ts'O, P. O. P., Biochemistry 16, 1239-1250 (1977)). Phosphate methylated (P-methoxy) oligonucleotides were synthesized and found to possess resistance towards endonuclease digestion (Gallo, K. L., et al. Nucl. Acid Res. 18, 7405 (1986)). A P-methoxy 18-mer oligonucleotide was shown to have high Tm value in duplexes with natural DNA and blocked to the DNA replication process at room temperature (Moody, H. M., et al., Nucl. Acid Res. 17, 4769-4782 (1989)). Moody et al. stated that phosphate ethylated (P-ethoxy) oligonucleotides would have poor antisense properties. P-methoxy dimers of DNA bases were synthesized using transient protecting group of FMOC for the exocyclic amino groups (Koole, L. H., et al., J. Org. Chem. 54, 1657-1664 (1989)).
Synthesis and physico-chemical properties of partial P-methoxy oligodeoxyribonucleotides were determined. Only the thymidine and cytidine oligomers with methyl phosphotriester could be prepared satisfactorily due to difficulty in maintaining methyl triester intact. Furthermore, the methyl group was found to have destabilizing effect on the hybridization properties of the modified oligomers with its complementary sequence by comparison with unmodified parent oligodeoxynucleotide (Vinogradeov, S., Asseline, U., Thoung, N. T., Tet. Let. 34, 5899-5902 (1993)).
Other reports have suggested that P-methoxy oligonucleotides are preferable to P-ethoxy as antisense olgionucleotides because of p-methoxy oligonucleotides showed stronger hybridization than methyl phosphonate or P-ethoxy oligonucleotides (van Genderen, M. H. P., et al., Kon. Ned. Akad. van Wetensch. B90, 155-159 (1987); van Genderen, M. H. P., et al., Trav. Chim. Pays Bas 108, 28-35 (1989)). P-ethoxy oligonucleotides were reported by van Genderen et al. to hybridize poorly to DNA, for which reason they were regarded unfavorably as antisense oligonucleotides (Moody, H. M., et al., Nucl. Acid Res. 17, 4769-4782 (1989)).
P-isopropoxyphosphoramidites have been synthesized from several nucleosides (Stec, W. J., et al., Tet. Let. 26, 2191-2194 (1985)), and a few short oligonucleotides containing P-isopropoxy phosphotriesters were synthesized, and hybridization studies were carried out.
U.S. Pat. No. 5,525,719 to Srivastava, S., and Raza, S. K., Jun. 11, 1996, suggests antisense oligonucleotides consisting of 2′-O-Methyl nucleotides linked by phosphodiester and/or P-ethoxy or P-methoxy, phosphotriester moieties.
Thus, currently there are no nucleic acid chemistries nor any chimeras that have been developed that optimally achieve all the features that are needed to provide an effective antisense oligonucleotide i.e. low toxicity, high specificity, nuclease resistance, ease of synthesis, RNAse H compatibility.